Nextflow workflow report

Workflow execution completed unsuccessfully!

The exit status of the task that caused the workflow execution to fail was: 255.

The full error message was:

Error executing process > 'NFCORE_METHYLSEQ:METHYLSEQ:BISMARK:BISMARK_ALIGN (zr3644_9)'

Caused by:
  Process `NFCORE_METHYLSEQ:METHYLSEQ:BISMARK:BISMARK_ALIGN (zr3644_9)` terminated with an error exit status (255)


Command executed:

  ln -sf $(readlink GCF_963853765.1_xbMagGiga1.1_genomic.fa) BismarkIndex/GCF_963853765.1_xbMagGiga1.1_genomic.fa
  
  bismark \
      -1 zr3644_9_R1_val_1_val_1_val_1.fq.gz -2 zr3644_9_R2_val_2_val_2_val_2.fq.gz \
      --genome BismarkIndex \
      --bam \
      --bowtie2    --non_directional --multicore 2
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_METHYLSEQ:METHYLSEQ:BISMARK:BISMARK_ALIGN":
      bismark: $(echo $(bismark -v 2>&1) | sed 's/^.*Bismark Version: v//; s/Copyright.*$//')
  END_VERSIONS

Command exit status:
  255

Command output:
  chr NC_088853.1 (76070991 bp)
  chr NC_088854.1 (61469542 bp)
  chr NC_088855.1 (61039741 bp)
  chr NC_088856.1 (57946171 bp)
  chr NC_088857.1 (57274926 bp)
  chr NC_088858.1 (56905015 bp)
  chr NC_088859.1 (53672946 bp)
  chr NC_088860.1 (51133819 bp)
  chr NC_088861.1 (50364239 bp)
  chr NC_088862.1 (37310742 bp)
  chr NW_027062568.1 (15579 bp)
  chr NW_027062569.1 (16498 bp)
  chr NW_027062570.1 (4000 bp)
  chr NW_027062571.1 (36893 bp)
  chr NW_027062572.1 (51000 bp)
  chr NW_027062573.1 (2000 bp)
  chr NW_027062574.1 (37061 bp)
  chr NW_027062575.1 (49428 bp)
  chr NW_027062576.1 (49232 bp)
  chr NW_027062577.1 (17087 bp)
  chr NW_027062578.1 (34507 bp)
  chr NW_027062579.1 (64000 bp)
  chr NW_027062580.1 (24229 bp)
  chr NW_027062581.1 (5000 bp)
  chr NW_027062582.1 (18808 bp)
  chr NW_027062583.1 (1000 bp)
  chr NW_027062584.1 (74000 bp)
  chr NW_027062585.1 (39334 bp)
  chr NW_027062586.1 (258015 bp)

Command error:
  
  
  >>> Writing bisulfite mapping results to zr3644_9_R1_val_1_val_1_val_1.fq.gz.temp.2_bismark_bt2_pe.bam <<<
  
  
  Reading in the sequence files zr3644_9_R1_val_1_val_1_val_1.fq.gz.temp.1 and zr3644_9_R2_val_2_val_2_val_2.fq.gz.temp.1
  
  Reading in the sequence files zr3644_9_R1_val_1_val_1_val_1.fq.gz.temp.2 and zr3644_9_R2_val_2_val_2_val_2.fq.gz.temp.2
  Processed 1000000 sequence pairs so far
  Processed 1000000 sequence pairs so far
  Processed 2000000 sequence pairs so far
  Processed 2000000 sequence pairs so far
  Processed 3000000 sequence pairs so far
  Processed 3000000 sequence pairs so far
  Processed 4000000 sequence pairs so far
  Processed 5000000 sequence pairs so far
  Processed 4000000 sequence pairs so far
  Processed 5000000 sequence pairs so far
  Chromosomal sequence could not be extracted for	A00742:173:HMGVGDSXY:2:1363:19651:25692_1:N:0:TGTCGCTG+AGTCAGAC	NW_027062580.1	24116
  Processed 6000000 sequence pairs so far
  Processed 6000000 sequence pairs so far
  Processed 7000000 sequence pairs so far
  Processed 7000000 sequence pairs so far
  Processed 8000000 sequence pairs so far
  Processed 8000000 sequence pairs so far
  Processed 9000000 sequence pairs so far
  Processed 9000000 sequence pairs so far
  Processed 10000000 sequence pairs so far
  Processed 10000000 sequence pairs so far
  Processed 11000000 sequence pairs so far
  Processed 11000000 sequence pairs so far
  Processed 12000000 sequence pairs so far
  Processed 13000000 sequence pairs so far
  Processed 12000000 sequence pairs so far
  Processed 13000000 sequence pairs so far
  (ERR): bowtie2-align died with signal 9 (KILL) 
  23786833 reads; of these:
    23786833 (100.00%) were paired; of these:
      19935805 (83.81%) aligned concordantly 0 times
      2106045 (8.85%) aligned concordantly exactly 1 time
      1744983 (7.34%) aligned concordantly >1 times
  16.19% overall alignment rate
  Processed 14000000 sequence pairs so far
  Processed 15000000 sequence pairs so far
  Processed 16000000 sequence pairs so far
  Use of uninitialized value $flag_2 in numeric eq (==) at /usr/local/bin/bismark line 3289, <__ANONIO__> line 26377711.
  Chromosome number extraction failed for *
  (ERR): bowtie2-align died with signal 13 (PIPE) 
  (ERR): bowtie2-align died with signal 13 (PIPE) 
  (ERR): bowtie2-align died with signal 13 (PIPE) 

Work dir:
  /mmfs1/gscratch/scrubbed/strigg/analyses/20250331_methylseq/work/8f/86b273d20b9091c4a4d12c42d604a1

Container:
  /gscratch/scrubbed/srlab/.apptainer/depot.galaxyproject.org-singularity-bismark-0.24.2--hdfd78af_0.img

Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh`